mri-publication-tools

MRI Agent Skills

Portable MRI analysis skill package centered on one standards-based skill:

• skills/multimodal-mri-publication-pipeline

This repository is set up for three delivery modes:

• Codex skill bundle
• OpenCode skill bundle
• Claude Code skill bundle plus a lightweight plugin marketplace

Install

Use the helper script from the repository root:

./install.sh codex
./install.sh claude
./install.sh opencode
./install.sh all

Add --link if you want a symlink instead of a copied folder while iterating locally.

This installs the skill into:

• Codex: ~/.codex/skills/
• Claude Code skills: ~/.claude/skills/
• OpenCode: ~/.config/opencode/skills/

Claude Code Plugin Use

This repository also exposes a Claude Code plugin manifest at .claude-plugin/plugin.json and a single-plugin marketplace at .claude-plugin/marketplace.json.

Local development:

claude --plugin-dir .
claude plugin validate .

After publishing to GitHub, add and install from Claude Code:

/plugin marketplace add owner/repo
/plugin install mri-publication-tools@mri-agent-skills

Replace owner/repo with your published repository.

GitHub Publishing

When you are ready to publish:

git init
git add .
git commit -m "Add multimodal MRI publication skill"
gh repo create mri-agent-skills --source . --public --push

If you want Codex to install directly from GitHub later, the skill path is:

skills/multimodal-mri-publication-pipeline

If you prefer a private repository, replace --public with --private.

What the skill covers

• raw DICOM to BIDS organization
• structural MRI
• resting-state fMRI
• task fMRI
• functional connectivity
• diffusion MRI and tractography
• QC, statistics, publication figures, three-line tables, and result writing